Align Carbamoyl-phosphate synthase small chain; EC 6.3.5.5; Carbamoyl-phosphate synthetase glutamine chain (uncharacterized)
to candidate 350059 BT0531 anthranilate synthase component II (NCBI ptt file)
Query= curated2:Q8KGA2 (366 letters) >FitnessBrowser__Btheta:350059 Length = 188 Score = 70.5 bits (171), Expect = 3e-17 Identities = 54/174 (31%), Positives = 83/174 (47%), Gaps = 15/174 (8%) Query: 181 AFDYGIKTNIIRQLNAEGCKVTVVNAKTTADEVLAMNPDGIFLSNGPGDPFAVTYAIDTI 240 +F Y + + +++L A +V V N + DEV D I LS GPG P + I Sbjct: 11 SFTYNL-LHAVKELGATDVEV-VRNDQINLDEVERF--DKIILSPGPGIPEEAGLLLPII 66 Query: 241 RELAARNSTLPIFGICLGHQLLSLAFGAKTYKLKFGHHGANHPVKNLLSNTI------EI 294 + A S I G+CLGHQ + AFGA+ LK +HG P+ L + + EI Sbjct: 67 KRYAPTKS---ILGVCLGHQAIGEAFGARLENLKEVYHGVQTPISILQKDVLFEGLGKEI 123 Query: 295 -TSQNHGFAVEMESLPGELELTHKNLYDMTVEGIRHRELPCFSVQYHPEAAPGP 347 + H + V E P LE+T ++ + + +RH+ +Q+HPE+ P Sbjct: 124 PVGRYHSWVVSREGFPECLEITAES-QEGQIMALRHKTYDVHGIQFHPESVLTP 176 Lambda K H 0.317 0.134 0.387 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 188 Number of extensions: 10 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 366 Length of database: 188 Length adjustment: 25 Effective length of query: 341 Effective length of database: 163 Effective search space: 55583 Effective search space used: 55583 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory